Distances on MDAnalysis

[Maria Thereza]

Hi everyone,

I was wondering how exactly distances are calculated on MDAnalysis. For example, if one is to calculate the RDF of an atom with respect to other group of atoms in solution, is the distance calculated between the center of mass,es or geometric centers, of the atoms? Or when calculating hydrogen bonds, is the distance between the donor atom and the acceptor atom related to the center of these atoms?

I tried to look it up on the library's code but I am still a little confused.

Thank you!

Best,

Maria

[Oliver Beckstein]

Hi Maria,

On Dec 15, 2023, at 07:54, Maria Thereza <mariath...@gmail.com> wrote:

Hi everyone,

I was wondering how exactly distances are calculated on MDAnalysis. For example, if one is to calculate the RDF of an atom with respect to other group of atoms in solution, is the distance calculated between the center of mass,es or geometric centers, of the atoms?

It depends on the analysis function. InterRDF() describes in detail that it will calculate atom-atom distances.

Atoms are considered point-like particles with the mass concentrated at the position, therefore there’s only Atom.position and no center of mass or center of geometry as these all conincide with the position.

In particular, distances are never calculated “between the surfaces of atoms” because we don’t know what “surface of an atom” means. Distances are always between atom positions (which you can think of as the “center” of the atom particle).

Or when calculating hydrogen bonds, is the distance between the donor atom and the acceptor atom related to the center of these atoms?

Yes, in the sense that “center” is simply the position of the atom.

I tried to look it up on the library's code but I am still a little confused.

I think the key idea here is that all our particles are point-like. If you want to consider the volume of atoms then you have to do extra work, but MDAnalysis keeps it simple as point-like particles.

Best,

Oliver

Thank you!

Best,

Maria

--

Oliver Beckstein (he/his/him)

email: orbe...@mdanalysis.org
twitter: @orbeckst

GitHub: @orbeckst

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